EC-comparator

Comparing cycle decompositions across technologies and methods.

Installation

Please install python3.9 and run the following code to install all dependencies:

bash cd AmpliconComparison mamba env create -f environment.yml conda activate comparator python -m pip install -r requirements.txt

And build and install (for developers):

```bash python -m pip install build installer toml setuptools

cd EC-comparator python -m build python -m pip install --force-reinstall dist/EC-comparator-0.0.2-py3-none-any.whl ```

Usage

Run the following test:

bash cd EC-comparator/AmpliconComparison python main.py -a ../examples/ecdna1/true.bed \ -b ../examples/ecdna1/reconstructed.bed \ -d ../examples/ecdna1/output

Output description

bash ../examples/ecdna1/output/ |-- breakpoints_profile_s1.txt |-- breakpoints_profile_s2.txt |-- coverage_breakpoints_profile.png |-- coverage_profile.png |-- coverage_profile_s1.txt |-- e1_coverage_profile.txt |-- e2_coverage_profile.txt |-- metrics.json |-- report.html |-- total_cost.png |-- total_cost_table.png

Help

```bash usage: EC-comparator [-h] -a FIRSTSTRUCTURE -b SECONDSTRUCTURE -d OUTDIR [--plot | --no-plot] [--report | --no-report] [--cn-hamming-dist CNHAMMINGDIST] [--cn-cosine-dist CNCOSINEDIST] [--cn-jc-dist CNJCDIST] [--fragments-dist FRAGMENTS_DIST] [--cycles-dist CYCLESDIST] [--breakpoint-dist BREAKPOINTDIST]

EC-comparator - compare cycle sets

optional arguments: -h, --help show this help message and exit -a FIRSTSTRUCTURE, --first-structure FIRSTSTRUCTURE First structure (bed format) -b SECONDSTRUCTURE, --second-structure SECONDSTRUCTURE Second structure (bed format) -d OUTDIR, --outdir OUTDIR Output directory --plot, --no-plot Plot coverage profiles --report, --no-report Generate report (this will set 'plot' also on True) --cn-hamming-dist CNHAMMINGDIST Hamming distance between genomic footprint. Recommended when no copy-number information available (default: True) --cn-cosine-dist CNCOSINEDIST Cosine distance between the coverage profile. --cn-jc-dist CNJCDIST Min-max distance / Jaccard distance between the coverage profile. --fragments-dist FRAGMENTSDIST Quantify the distance between fragments. --cycles-dist CYCLESDIST Quantify the distance between cycles. --breakpoint-dist BREAKPOINT_DIST Quantify the distance between cycles.

```

License

tbd